External Email - Use Caution
Dear madam or sir, I'm a student in China who use the Freesurfer to analyse my fMRI data and overlay some results on the surface. I met some problems about registration when I map my retinotopic results on the surface. I analysed the retinotopy by the analysePRF toolbox of Kendrick Kay, and the sulutions are matrix, the rows are voxels and the column is polar angle or eccentricity. So I replaced the BOLD values by the solutions in a volume image, for example, the polar angle solution, and I used it as overlay volume image, meanwhile I used the original volume image which is same but BOLD value didn't been changed as the template image to register, but whichever methods listed in the multimodal registration I used, the overlay volume image couldn't been overlaid in correct position on the inflated surface by freeview, just like the pic1.png in the attachment, at the same time the overlay volume image could been overlaid on the orig surface in correct position like the pic2.png in the attachment, so my first problem is why the inflated surface couldn't be overlaid correctly but the orig surface could be with the same registration data and what can I do to make the overlay volume image overlay on the inflated surface in correct position by freeview? Moreover I also used tksurfer to overlay, fortunately the overlay volume image could overlay on the inflated surface in correct position. But the overlay color scale couldn't be color wheel like the red-green-blue. Furthermore, the display in the tksurfer is upside down just like the pic3.png in the attachment. So my second problem is if there are some ways to make the tksurfer color scale like the freeview and how to make the tksurfer display correctly? Best regards, Qing Zhu
Try using mri_vol2surf to sample your fMRI onto the surface, then load it as a surface overlay in freeview
On 11/29/2019 3:35 AM, 朱青 wrote:
External Email - Use Caution
Dear madam or sir, I'm a student in China who use the Freesurfer to analyse my fMRI data and overlay some results on the surface. I met some problems about registration when I map my retinotopic results on the surface. I analysed the retinotopy by the analysePRF toolbox of Kendrick Kay, and the sulutions are matrix, the rows are voxels and the column is polar angle or eccentricity. So I replaced the BOLD values by the solutions in a volume image, for example, the polar angle solution, and I used it as overlay volume image, meanwhile I used the original volume image which is same but BOLD value didn't been changed as the template image to register, but whichever methods listed in the multimodal registration I used, the overlay volume image couldn't been overlaid in correct position on the inflated surface by freeview, just like the pic1.png in the attachment, at the same time the overlay volume image could been overlaid on the orig surface in correct position like the pic2.png in the attachment, so my first problem is why the inflated surface couldn't be overlaid correctly but the orig surface could be with the same registration data and what can I do to make the overlay volume image overlay on the inflated surface in correct position by freeview? Moreover I also used tksurfer to overlay, fortunately the overlay volume image could overlay on the inflated surface in correct position. But the overlay color scale couldn't be color wheel like the red-green-blue. Furthermore, the display in the tksurfer is upside down just like the pic3.png in the attachment. So my second problem is if there are some ways to make the tksurfer color scale like the freeview and how to make the tksurfer display correctly? Best regards, Qing Zhu
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freesurfer@nmr.mgh.harvard.edu
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Greve, Douglas N.,Ph.D. -
朱青